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rost@columbia.edu ret concise ret html # paho_chick MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
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Pattern-ID: CAMP_PHOSPHO_SITE PS00004 PDOC00004
Pattern-DE: cAMP- and cGMP-dependent protein kinase phosphorylation site
Pattern: [RK]{2}.[ST]
63 RRSS
Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern: [ST].[RK]
66 SSR
Pattern-ID: TYR_PHOSPHO_SITE PS00007 PDOC00007
Pattern-DE: Tyrosine kinase phosphorylation site
Pattern: [RK].{2,3}[DE].{2,3}Y
44 RFYNDLQQY
Pattern-ID: AMIDATION PS00009 PDOC00009
Pattern-DE: Amidation site
Pattern: .G[RK][RK]
61 YGRR
Pattern-ID: PANCREATIC_HORMONE PS00265 PDOC00238
Pattern-DE: Pancreatic hormone family signature
Pattern: [FY].{3}[LIVM].{2}Y.{3}[LIVMFY].R.R[YF]
45 FYNDLQQYLNVVTRHRY
>prot , (#) ppOld, paho_chick t1
MPPRWxxxxxxxxxxxxxx
VPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHR
YGRRSSSRVLCEEPMGAAGC
Identities computed with respect to: (query) prot Colored by: consensus/70% and sequence
HSP processing: ranked
3 [ . . . . : . ] 64
prot (#) ppOld, paho_chick t1 score P(N) N 100.0% PRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRR
1 PD001267 p99.2 (53) PAHO(22) PYY(13)... 112 2.6e-11 1 51.4% ------------------------PPEPEYPGDDATPEELAQYYAELRHYINLITRPRY---
2 PD041507 p99.2 (2) F13A(1) O08619(1)... 46 0.0013 2 40.5% --------------------GAIPPNNSNAAGDDLPTEDL-----NLQDYLNVTAVHLFKER
3 PD123104 p99.2 (1) O00634_HUMAN // N... 59 0.025 1 36.1% PGWPWGLLLTAGTLFAALSPGPPAPADPCHDEGGAP--------------------------
consensus/100% ........................Pspsphstsshs..........................
consensus/90% ........................Pspsphstsshs..........................
consensus/80% ........................Pspsphstsshs..........................
consensus/70% ....................Gs.sPspPsasGDDAPsE-L.....pLppYlNlhsh.ha...
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--- ------------------------------------------------------------ --- --- Again: these results were obtained based on the domain data- --- base collected by Daniel Kahn and his coworkers in Toulouse. --- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- The general WWW page is on: ---- --------------------------------------- --- http://www.toulouse.inra.fr/prodom.html ---- --------------------------------------- --- --- For WWW graphic interfaces to PRODOM, in particular for your --- protein family, follow the following links (each line is ONE --- single link for your protein!!): --- http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD001267 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD001267 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD001267 ==> graphical output of all proteins having domain PD001267 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD041507 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD041507 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD041507 ==> graphical output of all proteins having domain PD041507 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD123104 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD123104 http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD123104 ==> graphical output of all proteins having domain PD123104 --- --- NOTE: if you want to use the link, make sure the entire line --- is pasted as URL into your browser! --- --- END of PRODOM --- ------------------------------------------------------------
--- ------------------------------------------------------------ --- MAXHOM multiple sequence alignment --- ------------------------------------------------------------ --- --- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY --- ID : identifier of aligned (homologous) protein --- STRID : PDB identifier (only for known structures) --- PIDE : percentage of pairwise sequence identity --- WSIM : percentage of weighted similarity --- LALI : number of residues aligned --- NGAP : number of insertions and deletions (indels) --- LGAP : number of residues in all indels --- LSEQ2 : length of aligned sequence --- ACCNUM : SwissProt accession number --- NAME : one-line description of aligned protein --- --- MAXHOM ALIGNMENT HEADER: SUMMARY ID STRID IDE WSIM LALI NGAP LGAP LEN2 ACCNUM NAME paho_chick 1PPT 100 100 80 0 0 80 P01306 PANCREATIC HORMONE PRECUR paho_larar 94 97 36 0 0 36 P41337 PANCREATIC HORMONE (PANCR paho_strca 89 96 36 0 0 36 P11967 PANCREATIC HORMONE (PANCR paho_allmi 80 87 35 0 0 36 P06305 PANCREATIC HORMONE (PANCR paho_ansan 72 73 36 0 0 36 P06304 PANCREATIC HORMONE (PANCR neuy_sheep 60 78 35 0 0 36 P14765 NEUROPEPTIDE Y (NPY). neuy_human 1RON 46 64 69 0 0 97 P01303 NEUROPEPTIDE Y PRECURSOR neuy_chick 45 65 71 0 0 97 P28673 NEUROPEPTIDE Y PRECURSOR neuy_pig 56 76 35 0 0 36 P01304 NEUROPEPTIDE Y (NPY). neuy_rat 45 63 67 0 0 98 P07808 NEUROPEPTIDE Y PRECURSOR neuy_xenla 42 62 69 0 0 97 P33689 NEUROPEPTIDE Y PRECURSOR. pyy_pig 54 73 35 0 0 36 P01305 PEPTIDE YY (PYY). neuy_rabit 54 75 35 0 0 36 P09640 NEUROPEPTIDE Y (NPY). paho_canfa 41 52 71 1 1 93 P01299 PANCREATIC HORMONE PRECUR npy_lamfl 40 53 70 1 3 104 P48097 NEUROPEPTIDE Y PRECURSOR pyy_rat 39 53 75 1 2 98 P10631 PEPTIDE YY PRECURSOR (PYY paho_human 39 54 72 1 2 95 P01298 PANCREATIC HORMONE PRECUR neuy_ranri 51 73 35 0 0 36 P29949 (NPY). pyy_amica 51 72 35 0 0 36 P29205 PEPTIDE YY-LIKE (PYY). neuy_torma 38 57 71 0 0 98 P28674 NEUROPEPTIDE Y PRECURSOR paho_rat 39 49 67 2 8 98 P06303 PANCREATIC HORMONE PRECUR paho_mouse 38 50 69 2 6 100 P10601 PANCREATIC HORMONE PRECUR pyy_human 35 52 79 0 0 97 P10082 PEPTIDE YY PRECURSOR (PYY pyy_lamfl 38 50 63 1 1 93 P48098 PEPTIDE YY HOMOLOG PRECUR paho_bovin 1BBA 35 49 77 1 2 131 P01302 PANCREATIC HORMONE PRECUR paho_rante 49 66 35 0 0 36 P31229 PANCREATIC HORMONE (PANCR paho_rabit 49 68 35 0 0 36 P41336 PANCREATIC HORMONE (PANCR pyy_rajrh 49 71 35 0 0 36 P29206 PEPTIDE YY-LIKE (PYY). pyy_lepsp 49 71 35 0 0 36 P09473 PEPTIDE YY-LIKE (PYY) (NE pyy_oncki 49 70 35 0 0 36 P09474 PEPTIDE YY-LIKE (PYY). neuy_oncmy 49 70 35 0 0 36 P29071 NEUROPEPTIDE Y (NPY). pyy_bovin 36 54 67 0 0 97 P51694 PEPTIDE YY PRECURSOR (PYY paho_cavpo 37 52 63 1 3 126 P13083 PANCREATIC HORMONE PRECUR neuy_carau 34 52 71 0 0 96 P28672 NEUROPEPTIDE Y PRECURSOR paho_didma 46 66 35 0 0 36 P18107 PANCREATIC HORMONE (PANCR paho_macmu 46 66 35 0 0 36 P33684 PANCREATIC HORMONE (PANCR paho_ranca 46 64 35 0 0 36 P15427 PANCREATIC HORMONE (PANCR neuy_gadmo 46 69 35 0 0 36 P80167 NEUROPEPTIDE Y (NPY). paho_pig 46 66 35 0 0 36 P01300 PANCREATIC HORMONE (PANCR pyy_chick 43 65 37 0 0 37 P29203 PEPTIDE YY-LIKE (PYY). paho_felca 37 56 52 0 0 66 P06884 PANCREATIC HORMONE PRECUR paho_sheep 36 57 50 0 0 59 P01301 PANCREATIC HORMONE PRECUR paho_equze 43 65 35 0 0 36 P38000 PANCREATIC HORMONE (PANCR paho_erieu 43 65 35 0 0 36 P41335 PANCREATIC HORMONE (PANCR paho_tappi 43 65 35 0 0 36 P39659 PANCREATIC HORMONE (PANCR pyy_ranri 43 65 35 0 0 36 P29204 PEPTIDE YY-LIKE (PYY). spyy_phybi 43 65 35 0 0 36 P80952 SKIN PEPTIDE TYROSINE-TYR paho_cersi 43 65 35 0 0 36 P37999 PANCREATIC HORMONE (PANCR ppy_lopam 40 56 40 0 0 69 P09475 PANCREATIC POLYPEPTIDE YG --- --- MAXHOM ALIGNMENT: IN MSF FORMAT
--- ------------------------------------------------------------ --- 3D homologue: the known structure that appeared to have sig- --- 3D homologue: nificant sequence identity to your protein is: --- 3D homologue: 1PPT, 1RON, 1BBA, . --- 3D homologue: Note: we do NOT check whether the similarity --- 3D homologue: is in the region for which structure has --- 3D homologue: been determined. Thus, please verify! --- ------------------------------------------------------------
--- --- Version of database searched for alignment: --- SWISS-PROT release 38.0 (7/99) with 80000 proteins ---
Identities computed with respect to: (1) t10 Colored by: consensus/70% and sequence
1 [ . . . . : . . ] 80
1 t10 100.0% MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
2 paho_chick 100.0% MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
3 paho_larar 94.4% -------------------------GPVQPTYPGDDAPVEDLVRFYNDLQQYLNVVTRHRY-------------------
4 paho_strca 88.9% -------------------------GPAQPTYPGDDAPVEDLVRFYDNLQQYLNVVTRHRY-------------------
5 paho_allmi 80.0% --------------------------PLQPKYPGDGAPVEDLIQFYDDLQQYLNVVTRPRF-------------------
6 paho_ansan 72.2% -------------------------GPSQPTYPGNDAPVEDLRFYYDNLQQYRLNVFRHRY-------------------
7 neuy_sheep 60.0% --------------------------PSKPDNPGDDAPAEDLARYYSALRHYINLITRQRY-------------------
8 neuy_human 46.4% ------SGLTLALSLLVCLGALAEAYPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
9 neuy_chick 45.1% ----WVSVLTFALSLLICLGTLAEAYPSKPDSPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
10 neuy_pig 57.1% --------------------------PSKPDNPGEDAPAEDLARYYSALRHYINLITRQRY-------------------
11 neuy_rat 44.8% --------LTLALSLLVCLGILAEGYPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
12 neuy_xenla 42.0% ----WMSVLTLCLSMLICLGTFAEAYPSKPDNPGEDAPAEDMAKYYSALRHYINLITRQRYGKRSSPETMLSD-------
13 pyy_pig 54.3% --------------------------PAKPEAPGEDASPEELSRYYASLRHYLNLVTRQRY-------------------
14 neuy_rabit 54.3% --------------------------PSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY-------------------
15 paho_canfa 39.4% -------LLLSACVALLLQPPLgrGAPLEPVYPGDDATPEQMAQYAAELRRYINMLTRPRYGKRDRGEMRDILEWGSP--
16 npy_lamfl 38.6% -----ARVWLCAIALCLLaaRGAAAFPNKPDSPGEDAPAEDLARYLSAVRHYINLITRQRYGKRTLTEPYVPEFI-----
17 pyy_rat 37.3% VAVRRPWPVMVAMLLVLLagALVDAYPAKPEAPGEDASPEELSRYYASLRHYLNLVTRQRYGKREVPAALFSKLL-----
18 paho_human 38.9% ------SLLLLStaLLLQPLLGAQGAPLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRYGKRHKEDTLAFSEWGSP--
19 neuy_ranri 51.4% --------------------------PSKPDNPGEDAPAEDMAKYYSALRHYINLITRQRY-------------------
20 pyy_amica 51.4% --------------------------PPKPENPGEDAPPEELARYYTALRHYINLITRQRY-------------------
21 neuy_torma 38.0% ----WLGVFTFAFCMLICIGTFADAYPSKPDNPGEGAPAEDLAKYYSALRHYINLITRQRYGKRSSPEALMMTDL-----
22 paho_rat 35.6% ------SLFLLStaLLLQPLQGAWGAPLEPMYPGDYATHEQRAQYETQLRRYINTLTRPRYGKRDE------DTAGLPG-
23 paho_mouse 35.6% ------SLFLVStaLLLQPLQGTWGAPLEPMYPGDYATPEQMAQYETQLRRYINTLTRPRYGKRAEE----ENTGGLPG-
24 pyy_human 35.4% VRRPWPALTTVLLALLVCLGALVDAYPIKPEAPGEDASPEELNRYYASLRHYLNLVTRQRYGKRDGPDTLLSKTFFPDG-
25 pyy_lamfl 37.5% ---RLAALALSVCAILCLGMHA-SAFPPKPDNPGDNASPEQMARYKAAVRHYINLITRQRYGKRALT-------------
26 paho_bovin 35.1% -AHRCLFLLLLStaLLLQPPLGALGAPLEPEYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDKEGTLDFLECGSP--
27 paho_rante 48.6% --------------------------PSEPHHPGDQATQDQLAQYYSDLYQYITFVTRPRF-------------------
28 paho_rabit 48.6% --------------------------PPEPVYPGDDATPEQMAEYVADLRRYINMLTRPRY-------------------
29 pyy_rajrh 48.6% --------------------------PPKPENPGDDAAPEELAKYYSALRHYINLITRQRY-------------------
30 pyy_lepsp 48.6% --------------------------PPKPENPGEDAPPEELAKYYSALRHYINLITRQRY-------------------
31 pyy_oncki 48.6% --------------------------PPKPENPGEDAPPEELAKYYTALRHYINLITRQRY-------------------
32 neuy_oncmy 48.6% --------------------------PVKPENPGEDAPTEELAKYYTALRHYINLITRQRY-------------------
33 pyy_bovin 35.8% ---SWPAMATVLLTLLVCLGELVDAYPAKPQAPGEHASPDELNRYYTSLRHYLNLVTRQRFGKRDFSEAL----------
34 paho_cavpo 34.8% ----WLLLLGTCMALLL---PEAWGAPLEPVYPGDDATPQQMAQYAAEMRRYINMLTRPRYGKSAEEDAL----------
35 neuy_carau 33.8% ----WTGWAACAFLLFVCLGTLTEGYPTKPDNPGEGAPAEELAKYYSALRHYINLITRQRYGKRSSADTLISDLL-----
36 paho_didma 45.7% --------------------------PQEPVYPGDDATPEQMAKYAAELRRYINRLTRPRY-------------------
37 paho_macmu 45.7% --------------------------PLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRY-------------------
38 paho_ranca 45.7% --------------------------PSEPHHPGDQATPDQLAQYYSDLYQYITFITRPRF-------------------
39 neuy_gadmo 45.7% --------------------------PIKPENPGEDAPADELAKYYSALRHYINLITRQRY-------------------
40 paho_pig 45.7% --------------------------PLEPVYPGDDATPEQMAQYAAELRRYINMLTRPRY-------------------
41 pyy_chick 43.2% ------------------------AYPPKPESPGDAASPEEIAQYFSALRHYINLVTRQRY-------------------
42 paho_felca 36.5% --------------------------PLEPVYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDRGETLDILEWGSP--
43 paho_sheep 36.0% ----------------------------EPEYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDKEGTLDFLECGSP--
44 paho_equze 42.9% --------------------------PMEPVYPGDNATPEQMAQYAAELRRYINMLTRPRY-------------------
45 paho_erieu 42.9% --------------------------PLEPVYPGDNATPEQMAHYAAELRRYINMLTRPRY-------------------
46 paho_tappi 42.9% --------------------------PLEPVYPGDNATPEQMAQYAAELRRYINMLTRPRY-------------------
47 pyy_ranri 42.9% --------------------------PPKPENPGEDASPEEMTKYLTALRHYINLVTRQRY-------------------
48 spyy_phybi 42.9% --------------------------PPKPESPGEDASPEEMNKYLTALRHYINLVTRQRY-------------------
49 paho_cersi 42.9% --------------------------PLEPVYPGDNATPEEMAQYAAELRRYINMLTRPRY-------------------
50 ppy_lopam 40.0% --------------------------PPKPETPGSNASPEDWASYQAAVRHYVNLITRQRYGXXSS--------------
consensus/100% ............................pP..PGp.As.pph..a.sth.pYh..lhR.Ra...................
consensus/90% .......................P.pP..PG-sAssEphspYhstLppYlNhlTR.RY.................
consensus/80% ......................P.cP..PG-sAssEphupYhstLR+YlNhlTR.RY..............
consensus/70% ....................P.cPp.PG-sAssEphApYhusLR+YINhlTR.RY..............
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**************************************************************************** * * * PHD: Profile fed neural network systems from HeiDelberg * * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * * * * Prediction of: * * secondary structure, by PHDsec * * solvent accessibility, by PHDacc * * and helical transmembrane regions, by PHDhtm * * * * Author: * * Burkhard Rost * * EMBL, 69012 Heidelberg, Germany * * Internet: Rost@EMBL-Heidelberg.DE * * * * All rights reserved. * * * **************************************************************************** * * * The network systems are described in: * * * * PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. * * B Rost & C Sander: Proteins, 1994, 19, 55-72. * * PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. * * PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. * * * ****************************************************************************
| %H: 38.8 | %E: 0.0 | %L: 61.2 |
| %A: 8.8 | %C: 3.8 | %D: 5.0 | %E: 3.8 | %F: 1.2 |
| %G: 7.5 | %H: 1.2 | %I: 1.2 | %K: 0.0 | %L: 15.0 |
| %M: 2.5 | %N: 2.5 | %P: 11.2 | %Q: 3.8 | %R: 8.8 |
| %S: 7.5 | %T: 3.8 | %V: 6.2 | %W: 1.2 | %Y: 5.0 |
| AA : | amino acid sequence | |
| PHD_sec: | PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PHD = PHD: Profile network prediction HeiDelberg | |
| Rel_sec: | reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*' | |
| SUB_sec: | subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header) NOTE: for this subset the following symbols are used: L: is loop (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 5 | |
| pH_sec: | 'probability' for assigning helix (1=high, 0=low) | |
| pE_sec: | 'probability' for assigning strand (1=high, 0=low) | |
| pL_sec: | 'probability' for assigning neither helix, nor strand (1=high, 0=low) | |
| P_3_acc: | PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. | |
| Rel_acc: | reliability index for PHDacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*' | |
| SUB_acc: | subset of the PHDacc prediction, for all residues with an expected average correlation > 0.69 (tables in header) NOTE: for this subset the following symbols are used: I: is intermediate (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 4 | |
| PHD_acc: | PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%). |
PHD results (brief)....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8 AA MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC PHD_sec HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHH Rel_sec ** ************ ******************* **************** ************* ******** P_3_acc eeeebbbbbbbbbbbbbbeeeebee eeeee eeeebeeeebbebbbbb bbbbbbbbe bbeeeeeebbeeeeebeeee Rel_acc * * * ****** * * * ** **
PHD results (normal) ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8 AA MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC PHD_sec HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHH Rel_sec 99344667899999775148557799999899999999487899999999999963455558768757654478789999 SUB_sec LL...HHHHHHHHHHHH..LLLLLLLLLLLLLLLLLLL.HHHHHHHHHHHHHHHH..LLLLLLLLLLLLL..LLLLLLLL P_3_acc eeeebbbbbbbbbbbbbbeeeebee eeeee eeeebeeeebbebbbbb bbbbbbbbe bbeeeeeebbeeeeebeeee Rel_acc 31211425343546874000210210002011012131121533400071058235401101110232000112000210 SUB_acc .....b.b.b.bbbbbb........................b..b...b..bb..bb.......................
--- --- GLOBE: prediction of protein globularity --- --- nexp = 44 (number of predicted exposed residues) --- nfit = 42 (number of expected exposed residues --- diff = 2.00 (difference nexp-nfit) --- =====> your protein appears as compact, as a globular domain --- --- --- GLOBE: further explanations preliminaryily in: --- http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html --- --- END of GLOBE
END of results for file t1
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